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Added unit tests #10
Added unit tests #10
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The R CMD check results are below. You should try to make sure that everything is passing before a PR (draft or otherwise).
Most of the messages below are due to these issues:
- You have a lot of empty examples in the documentation. I would just take them out if you don't have them.
- There a many namespace issues. I would completely import
ggplot
,rlang
, anddplyr
. Otherwise, you should namespace everything (i.e., usetune::.get_tune_outcome_names
instead of just.get_tune_outcome_names
).- Most of the "no visible global function definition" notes are related to this.
- Also, whenever you use a function from the package, it needs to be in the
Import
field of the DESCRIPTION file. You need to importplotly
andrlang
- Related to ☝️ , don't import
tidymodels
ortidyverse
. Figure out the specific packages that you need and import them.
- You should document your data objects, even just to say that they are internal objects used for development. See the R packages book for details.
- There are a few function arguments that are undocumented. I think that this can be solved by using more
@inheritParams
directives.
==> devtools::check()
ℹ Updating shinymodels documentation
ℹ Loading shinymodels
Registered S3 method overwritten by 'tune':
method from
required_pkgs.model_spec parsnip
Warning: [/Users/max/github/shinymodels/R/Misc.R:11] @examples requires a value
Warning: [/Users/max/github/shinymodels/R/Misc.R:34] @examples requires a value
Warning: [/Users/max/github/shinymodels/R/Misc.R:52] @examples requires a value
Warning: [/Users/max/github/shinymodels/R/regression_diag_plots.R:10] @examples requires a value
Warning: [/Users/max/github/shinymodels/R/regression_diag_plots.R:33] @examples requires a value
Warning: [/Users/max/github/shinymodels/R/regression_diag_plots.R:57] @examples requires a value
Warning: [/Users/max/github/shinymodels/R/regression_diag_plots.R:82] @examples requires a value
Warning: [/Users/max/github/shinymodels/R/two_class_diag_plots.R:9] @examples requires a value
Warning: [/Users/max/github/shinymodels/R/two_class_diag_plots.R:38] @examples requires a value
Warning: [/Users/max/github/shinymodels/R/two_class_diag_plots.R:61] @examples requires a value
Warning: [/Users/max/github/shinymodels/R/two_class_diag_plots.R:106] @examples requires a value
Warning: [/Users/max/github/shinymodels/R/two_class_diag_plots.R:149] @examples requires a value
Warning: [/Users/max/github/shinymodels/R/two_class_diag_plots.R:174] @examples requires a value
Writing NAMESPACE
Writing NAMESPACE
── Building ─────────────────────────────────────────────────────────────────────────────────────────── shinymodels ──
Setting env vars:
• CFLAGS : -Wall -pedantic -fdiagnostics-color=always
• CXXFLAGS : -Wall -pedantic -fdiagnostics-color=always
• CXX11FLAGS: -Wall -pedantic -fdiagnostics-color=always
──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✓ checking for file ‘/Users/max/github/shinymodels/DESCRIPTION’ ...
─ preparing ‘shinymodels’:
✓ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘shinymodels_0.0.0.9000.tar.gz’
── Checking ─────────────────────────────────────────────────────────────────────────────────────────── shinymodels ──
Setting env vars:
• _R_CHECK_CRAN_INCOMING_REMOTE_: FALSE
• _R_CHECK_CRAN_INCOMING_ : FALSE
• _R_CHECK_FORCE_SUGGESTS_ : FALSE
• NOT_CRAN : true
── R CMD check ─────────────────────────────────────────────────────────────────
─ using log directory ‘/Users/max/github/shinymodels.Rcheck’
─ using R version 4.1.0 (2021-05-18)
─ using platform: x86_64-apple-darwin17.0 (64-bit)
─ using session charset: UTF-8
─ using options ‘--no-manual --as-cran’
✓ checking for file ‘shinymodels/DESCRIPTION’
─ this is package ‘shinymodels’ version ‘0.0.0.9000’
─ package encoding: UTF-8
✓ checking package namespace information
✓ checking package dependencies (3.8s)
✓ checking if this is a source package ...
✓ checking if there is a namespace
✓ checking for executable files ...
✓ checking for hidden files and directories
✓ checking for portable file names
✓ checking for sufficient/correct file permissions
✓ checking serialization versions ...
✓ checking whether package ‘shinymodels’ can be installed (3.6s)
N checking installed package size ...
installed size is 6.6Mb
sub-directories of 1Mb or more:
data 6.5Mb
✓ checking package directory ...
✓ checking for future file timestamps (417ms)
N checking DESCRIPTION meta-information ...
Malformed Description field: should contain one or more complete sentences.
✓ checking top-level files ...
✓ checking for left-over files ...
✓ checking index information
✓ checking package subdirectories ...
✓ checking R files for non-ASCII characters ...
✓ checking R files for syntax errors ...
✓ checking whether the package can be loaded ...
✓ checking whether the package can be loaded with stated dependencies ...
✓ checking whether the package can be unloaded cleanly ...
✓ checking whether the namespace can be loaded with stated dependencies ...
✓ checking whether the namespace can be unloaded cleanly ...
✓ checking loading without being on the library search path ...
W checking dependencies in R code (1.8s)
'::' or ':::' imports not declared from:
‘plotly’ ‘rlang’
✓ checking S3 generic/method consistency (950ms)
✓ checking replacement functions ...
✓ checking foreign function calls ...
N checking R code for possible problems (2.1s)
first_class_prob_name: no visible global function definition for ‘sym’
organize_data: no visible global function definition for
‘.get_tune_outcome_names’
organize_data: no visible global function definition for
‘collect_predictions’
organize_data: no visible global function definition for ‘mutate’
organize_data: no visible global function definition for ‘sym’
organize_data: no visible binding for global variable ‘.pred’
organize_data: no visible global function definition for ‘inner_join’
organize_data: no visible global function definition for ‘add_rowindex’
organize_data: no visible global function definition for ‘select’
plot_numeric_obs_pred: no visible global function definition for
‘ggplot’
plot_numeric_obs_pred: no visible global function definition for ‘aes’
plot_numeric_obs_pred: no visible global function definition for ‘sym’
plot_numeric_obs_pred: no visible binding for global variable ‘.pred’
plot_numeric_obs_pred: no visible global function definition for
‘geom_abline’
plot_numeric_obs_pred: no visible global function definition for
‘geom_point’
plot_numeric_obs_pred: no visible binding for global variable ‘.color’
plot_numeric_obs_pred: no visible global function definition for
‘scale_color_identity’
plot_numeric_obs_pred: no visible global function definition for
‘coord_obs_pred’
plot_numeric_obs_pred: no visible global function definition for ‘labs’
plot_numeric_obs_pred: no visible global function definition for
‘theme_bw’
plot_numeric_obs_pred: no visible global function definition for
‘theme’
plot_numeric_obs_pred: no visible global function definition for
‘ggplotly’
plot_numeric_res_factorcol: no visible global function definition for
‘ggplot’
plot_numeric_res_factorcol: no visible global function definition for
‘aes’
plot_numeric_res_factorcol: no visible global function definition for
‘reorder’
plot_numeric_res_factorcol: no visible global function definition for
‘sym’
plot_numeric_res_factorcol: no visible binding for global variable
‘.residual’
plot_numeric_res_factorcol: no visible global function definition for
‘geom_point’
plot_numeric_res_factorcol: no visible global function definition for
‘geom_abline’
plot_numeric_res_factorcol: no visible binding for global variable
‘.color’
plot_numeric_res_factorcol: no visible global function definition for
‘scale_color_identity’
plot_numeric_res_factorcol: no visible global function definition for
‘coord_obs_pred’
plot_numeric_res_factorcol: no visible global function definition for
‘labs’
plot_numeric_res_factorcol: no visible global function definition for
‘theme_bw’
plot_numeric_res_factorcol: no visible global function definition for
‘theme’
plot_numeric_res_factorcol: no visible global function definition for
‘ggplotly’
plot_numeric_res_numcol: no visible global function definition for
‘ggplot’
plot_numeric_res_numcol: no visible global function definition for
‘aes’
plot_numeric_res_numcol: no visible global function definition for
‘sym’
plot_numeric_res_numcol: no visible binding for global variable
‘.residual’
plot_numeric_res_numcol: no visible global function definition for
‘geom_abline’
plot_numeric_res_numcol: no visible global function definition for
‘geom_point’
plot_numeric_res_numcol: no visible binding for global variable
‘.color’
plot_numeric_res_numcol: no visible global function definition for
‘scale_color_identity’
plot_numeric_res_numcol: no visible global function definition for
‘coord_obs_pred’
plot_numeric_res_numcol: no visible global function definition for
‘labs’
plot_numeric_res_numcol: no visible global function definition for
‘theme_bw’
plot_numeric_res_numcol: no visible global function definition for
‘theme’
plot_numeric_res_numcol: no visible global function definition for
‘ggplotly’
plot_numeric_res_pred: no visible global function definition for
‘ggplot’
plot_numeric_res_pred: no visible global function definition for ‘aes’
plot_numeric_res_pred: no visible global function definition for ‘sym’
plot_numeric_res_pred: no visible binding for global variable
‘.residual’
plot_numeric_res_pred: no visible global function definition for
‘geom_abline’
plot_numeric_res_pred: no visible global function definition for
‘geom_point’
plot_numeric_res_pred: no visible binding for global variable ‘.color’
plot_numeric_res_pred: no visible global function definition for
‘scale_color_identity’
plot_numeric_res_pred: no visible global function definition for
‘coord_obs_pred’
plot_numeric_res_pred: no visible global function definition for ‘labs’
plot_numeric_res_pred: no visible global function definition for
‘theme_bw’
plot_numeric_res_pred: no visible global function definition for
‘theme’
plot_numeric_res_pred: no visible global function definition for
‘ggplotly’
plot_twoclass_conf_mat: no visible global function definition for
‘augment’
plot_twoclass_conf_mat: no visible global function definition for
‘conf_mat’
plot_twoclass_conf_mat: no visible binding for global variable ‘Class’
plot_twoclass_conf_mat: no visible binding for global variable
‘.pred_class’
plot_twoclass_conf_mat: no visible global function definition for
‘autoplot’
plot_twoclass_obs_pred: no visible global function definition for
‘augment’
plot_twoclass_obs_pred: no visible global function definition for
‘ggplot’
plot_twoclass_obs_pred: no visible global function definition for ‘aes’
plot_twoclass_obs_pred: no visible global function definition for
‘geom_histogram’
plot_twoclass_obs_pred: no visible global function definition for
‘facet_wrap’
plot_twoclass_obs_pred: no visible global function definition for
‘labeller’
plot_twoclass_obs_pred: no visible binding for global variable
‘label_both’
plot_twoclass_obs_pred: no visible global function definition for
‘labs’
plot_twoclass_obs_pred: no visible global function definition for
‘lims’
plot_twoclass_pr: no visible global function definition for ‘augment’
plot_twoclass_pr: no visible global function definition for ‘pr_curve’
plot_twoclass_pr: no visible binding for global variable ‘Class’
plot_twoclass_pr: no visible global function definition for ‘mutate’
plot_twoclass_pr: no visible binding for global variable ‘.threshold’
plot_twoclass_pr: no visible global function definition for ‘arrange’
plot_twoclass_pr: no visible binding for global variable ‘delta’
plot_twoclass_pr: no visible global function definition for ‘slice’
plot_twoclass_pr: no visible global function definition for ‘autoplot’
plot_twoclass_pr: no visible global function definition for
‘geom_point’
plot_twoclass_pr: no visible global function definition for ‘aes’
plot_twoclass_pr: no visible binding for global variable ‘specificity’
plot_twoclass_pr: no visible binding for global variable ‘sensitivity’
plot_twoclass_pred_factorcol: no visible global function definition for
‘mutate’
plot_twoclass_pred_factorcol: no visible global function definition for
‘:=’
plot_twoclass_pred_factorcol: no visible global function definition for
‘case_when’
plot_twoclass_pred_factorcol: no visible global function definition for
‘ggplot’
plot_twoclass_pred_factorcol: no visible global function definition for
‘aes’
plot_twoclass_pred_factorcol: no visible global function definition for
‘sym’
plot_twoclass_pred_factorcol: no visible global function definition for
‘geom_point’
plot_twoclass_pred_factorcol: no visible binding for global variable
‘.color’
plot_twoclass_pred_factorcol: no visible global function definition for
‘facet_wrap’
plot_twoclass_pred_factorcol: no visible global function definition for
‘labeller’
plot_twoclass_pred_factorcol: no visible binding for global variable
‘label_both’
plot_twoclass_pred_factorcol: no visible global function definition for
‘scale_color_identity’
plot_twoclass_pred_factorcol: no visible global function definition for
‘labs’
plot_twoclass_pred_factorcol: no visible global function definition for
‘theme_bw’
plot_twoclass_pred_factorcol: no visible global function definition for
‘theme’
plot_twoclass_pred_factorcol: no visible global function definition for
‘ggplotly’
plot_twoclass_pred_numcol: no visible global function definition for
‘mutate’
plot_twoclass_pred_numcol: no visible global function definition for
‘:=’
plot_twoclass_pred_numcol: no visible global function definition for
‘case_when’
plot_twoclass_pred_numcol: no visible global function definition for
‘ggplot’
plot_twoclass_pred_numcol: no visible global function definition for
‘aes’
plot_twoclass_pred_numcol: no visible global function definition for
‘sym’
plot_twoclass_pred_numcol: no visible global function definition for
‘geom_point’
plot_twoclass_pred_numcol: no visible binding for global variable
‘.color’
plot_twoclass_pred_numcol: no visible global function definition for
‘facet_wrap’
plot_twoclass_pred_numcol: no visible global function definition for
‘labeller’
plot_twoclass_pred_numcol: no visible binding for global variable
‘label_both’
plot_twoclass_pred_numcol: no visible global function definition for
‘scale_color_identity’
plot_twoclass_pred_numcol: no visible global function definition for
‘labs’
plot_twoclass_pred_numcol: no visible global function definition for
‘theme_bw’
plot_twoclass_pred_numcol: no visible global function definition for
‘theme’
plot_twoclass_pred_numcol: no visible global function definition for
‘ggplotly’
plot_twoclass_roc: no visible global function definition for ‘augment’
plot_twoclass_roc: no visible global function definition for
‘roc_curve’
plot_twoclass_roc: no visible binding for global variable ‘Class’
plot_twoclass_roc: no visible global function definition for ‘mutate’
plot_twoclass_roc: no visible binding for global variable ‘.threshold’
plot_twoclass_roc: no visible global function definition for ‘arrange’
plot_twoclass_roc: no visible binding for global variable ‘delta’
plot_twoclass_roc: no visible global function definition for ‘slice’
plot_twoclass_roc: no visible global function definition for ‘autoplot’
plot_twoclass_roc: no visible global function definition for
‘geom_point’
plot_twoclass_roc: no visible global function definition for ‘aes’
plot_twoclass_roc: no visible binding for global variable ‘specificity’
plot_twoclass_roc: no visible binding for global variable ‘sensitivity’
Undefined global functions or variables:
.color .get_tune_outcome_names .pred .pred_class .residual .threshold
:= Class add_rowindex aes arrange augment autoplot case_when
collect_predictions conf_mat coord_obs_pred delta facet_wrap
geom_abline geom_histogram geom_point ggplot ggplotly inner_join
label_both labeller labs lims mutate pr_curve reorder roc_curve
scale_color_identity select sensitivity slice specificity sym theme
theme_bw
Consider adding
importFrom("stats", "reorder")
to your NAMESPACE file.
✓ checking Rd files ...
✓ checking Rd metadata ...
✓ checking Rd line widths ...
✓ checking Rd cross-references ...
W checking for missing documentation entries ...
Undocumented code objects:
‘ad_data_boost_res’ ‘ames_rf_res’ ‘mtcars_spline_res’ ‘volcano_res’
Undocumented data sets:
‘volcano_res’ ‘ames_rf_res’ ‘mtcars_spline_res’ ‘ad_data_boost_res’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
✓ checking for code/documentation mismatches (899ms)
W checking Rd \usage sections ...
Undocumented arguments in documentation object 'plot_numeric_res_factorcol'
‘dat’ ‘y_name’
Undocumented arguments in documentation object 'plot_numeric_res_numcol'
‘dat’ ‘y_name’
Undocumented arguments in documentation object 'plot_numeric_res_pred'
‘dat’ ‘y_name’
Undocumented arguments in documentation object 'plot_twoclass_obs_pred'
‘event_level’ ‘prob_bins’
Undocumented arguments in documentation object 'plot_twoclass_pr'
‘event_level’
Undocumented arguments in documentation object 'plot_twoclass_pred_factorcol'
‘event_level’ ‘prob_breaks’ ‘prob_eps’
Undocumented arguments in documentation object 'plot_twoclass_pred_numcol'
‘event_level’ ‘prob_breaks’ ‘prob_eps’
Undocumented arguments in documentation object 'plot_twoclass_roc'
‘event_level’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
✓ checking Rd contents (1s)
✓ checking for unstated dependencies in examples ...
✓ checking contents of ‘data’ directory (1s)
✓ checking data for non-ASCII characters (1.3s)
W checking LazyData
LazyData DB of 6.5 MB without LazyDataCompression set
See §1.1.6 of 'Writing R Extensions'
✓ checking data for ASCII and uncompressed saves ...
W checking files in ‘vignettes’
Files in the 'vignettes' directory but no files in 'inst/doc':
‘introduction.Rmd’
Package has no Sweave vignette sources and no VignetteBuilder field.
─ checking examples ... NONE
✓ checking for unstated dependencies in ‘tests’ ...
─ checking tests ...
✓ Running ‘spelling.R’
X Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ...
6,27d5
< Potential spelling errors:
< WORD FOUND IN
< ORCID shinymodels-package.Rd:16,17
< factorcol plot_numeric_res_factorcol.Rd:13
< plot_twoclass_pred_factorcol.Rd:26
< magrittr pipe.Rd:10,12
< numcol plot_numeric_res_numcol.Rd:13
< plot_twoclass_pred_numcol.Rd:26
< pred plot_numeric_obs_pred.Rd:16
< plot_numeric_res_pred.Rd:10
< plot_twoclass_conf_mat.Rd:13
< plot_twoclass_obs_pred.Rd:14
< plot_twoclass_pred_factorcol.Rd:26
< plot_twoclass_pred_numcol.Rd:26
< roc plot_twoclass_roc.Rd:5,13,16
< tidymodel plot_twoclass_pred_numcol.Rd:29
< twoclass plot_twoclass_conf_mat.Rd:13
< plot_twoclass_obs_pred.Rd:14
< plot_twoclass_pr.Rd:13
< plot_twoclass_pred_factorcol.Rd:26
< plot_twoclass_pred_numcol.Rd:26
< plot_twoclass_roc.Rd:13
E Running ‘testthat.R’ (4.3s)
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
Backtrace:
▆
1. ├─testthat::expect_error(organize_data(lin_mod, mtcars), "res_object should be a fit_resamples() object") test-organize_data.R:32:2
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat:::.capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─shinymodels::organize_data(lin_mod, mtcars)
8. ├─tune::collect_predictions(res_object, summarize = TRUE)
9. └─tune:::collect_predictions.default(res_object, summarize = TRUE) /Users/max/github/tune/R/collect.R:87:2
[ FAIL 3 | WARN 2 | SKIP 0 | PASS 3 ]
Error: Test failures
Execution halted
✓ checking for non-standard things in the check directory
✓ checking for detritus in the temp directory
See
‘/Users/max/github/shinymodels.Rcheck/00check.log’
for details.
── R CMD check results ───────────────────────────── shinymodels 0.0.0.9000 ────
Duration: 25.1s
> checking tests ...
See below...
> checking dependencies in R code ... WARNING
'::' or ':::' imports not declared from:
‘plotly’ ‘rlang’
> checking for missing documentation entries ... WARNING
Undocumented code objects:
‘ad_data_boost_res’ ‘ames_rf_res’ ‘mtcars_spline_res’ ‘volcano_res’
Undocumented data sets:
‘volcano_res’ ‘ames_rf_res’ ‘mtcars_spline_res’ ‘ad_data_boost_res’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
> checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'plot_numeric_res_factorcol'
‘dat’ ‘y_name’
Undocumented arguments in documentation object 'plot_numeric_res_numcol'
‘dat’ ‘y_name’
Undocumented arguments in documentation object 'plot_numeric_res_pred'
‘dat’ ‘y_name’
Undocumented arguments in documentation object 'plot_twoclass_obs_pred'
‘event_level’ ‘prob_bins’
Undocumented arguments in documentation object 'plot_twoclass_pr'
‘event_level’
Undocumented arguments in documentation object 'plot_twoclass_pred_factorcol'
‘event_level’ ‘prob_breaks’ ‘prob_eps’
Undocumented arguments in documentation object 'plot_twoclass_pred_numcol'
‘event_level’ ‘prob_breaks’ ‘prob_eps’
Undocumented arguments in documentation object 'plot_twoclass_roc'
‘event_level’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
> checking LazyData ... WARNING
LazyData DB of 6.5 MB without LazyDataCompression set
See §1.1.6 of 'Writing R Extensions'
> checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
‘introduction.Rmd’
Package has no Sweave vignette sources and no VignetteBuilder field.
> checking installed package size ... NOTE
installed size is 6.6Mb
sub-directories of 1Mb or more:
data 6.5Mb
> checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
> checking R code for possible problems ... NOTE
first_class_prob_name: no visible global function definition for ‘sym’
organize_data: no visible global function definition for
‘.get_tune_outcome_names’
organize_data: no visible global function definition for
‘collect_predictions’
organize_data: no visible global function definition for ‘mutate’
organize_data: no visible global function definition for ‘sym’
organize_data: no visible binding for global variable ‘.pred’
organize_data: no visible global function definition for ‘inner_join’
organize_data: no visible global function definition for ‘add_rowindex’
organize_data: no visible global function definition for ‘select’
plot_numeric_obs_pred: no visible global function definition for
‘ggplot’
plot_numeric_obs_pred: no visible global function definition for ‘aes’
plot_numeric_obs_pred: no visible global function definition for ‘sym’
plot_numeric_obs_pred: no visible binding for global variable ‘.pred’
plot_numeric_obs_pred: no visible global function definition for
‘geom_abline’
plot_numeric_obs_pred: no visible global function definition for
‘geom_point’
plot_numeric_obs_pred: no visible binding for global variable ‘.color’
plot_numeric_obs_pred: no visible global function definition for
‘scale_color_identity’
plot_numeric_obs_pred: no visible global function definition for
‘coord_obs_pred’
plot_numeric_obs_pred: no visible global function definition for ‘labs’
plot_numeric_obs_pred: no visible global function definition for
‘theme_bw’
plot_numeric_obs_pred: no visible global function definition for
‘theme’
plot_numeric_obs_pred: no visible global function definition for
‘ggplotly’
plot_numeric_res_factorcol: no visible global function definition for
‘ggplot’
plot_numeric_res_factorcol: no visible global function definition for
‘aes’
plot_numeric_res_factorcol: no visible global function definition for
‘reorder’
plot_numeric_res_factorcol: no visible global function definition for
‘sym’
plot_numeric_res_factorcol: no visible binding for global variable
‘.residual’
plot_numeric_res_factorcol: no visible global function definition for
‘geom_point’
plot_numeric_res_factorcol: no visible global function definition for
‘geom_abline’
plot_numeric_res_factorcol: no visible binding for global variable
‘.color’
plot_numeric_res_factorcol: no visible global function definition for
‘scale_color_identity’
plot_numeric_res_factorcol: no visible global function definition for
‘coord_obs_pred’
plot_numeric_res_factorcol: no visible global function definition for
‘labs’
plot_numeric_res_factorcol: no visible global function definition for
‘theme_bw’
plot_numeric_res_factorcol: no visible global function definition for
‘theme’
plot_numeric_res_factorcol: no visible global function definition for
‘ggplotly’
plot_numeric_res_numcol: no visible global function definition for
‘ggplot’
plot_numeric_res_numcol: no visible global function definition for
‘aes’
plot_numeric_res_numcol: no visible global function definition for
‘sym’
plot_numeric_res_numcol: no visible binding for global variable
‘.residual’
plot_numeric_res_numcol: no visible global function definition for
‘geom_abline’
plot_numeric_res_numcol: no visible global function definition for
‘geom_point’
plot_numeric_res_numcol: no visible binding for global variable
‘.color’
plot_numeric_res_numcol: no visible global function definition for
‘scale_color_identity’
plot_numeric_res_numcol: no visible global function definition for
‘coord_obs_pred’
plot_numeric_res_numcol: no visible global function definition for
‘labs’
plot_numeric_res_numcol: no visible global function definition for
‘theme_bw’
plot_numeric_res_numcol: no visible global function definition for
‘theme’
plot_numeric_res_numcol: no visible global function definition for
‘ggplotly’
plot_numeric_res_pred: no visible global function definition for
‘ggplot’
plot_numeric_res_pred: no visible global function definition for ‘aes’
plot_numeric_res_pred: no visible global function definition for ‘sym’
plot_numeric_res_pred: no visible binding for global variable
‘.residual’
plot_numeric_res_pred: no visible global function definition for
‘geom_abline’
plot_numeric_res_pred: no visible global function definition for
‘geom_point’
plot_numeric_res_pred: no visible binding for global variable ‘.color’
plot_numeric_res_pred: no visible global function definition for
‘scale_color_identity’
plot_numeric_res_pred: no visible global function definition for
‘coord_obs_pred’
plot_numeric_res_pred: no visible global function definition for ‘labs’
plot_numeric_res_pred: no visible global function definition for
‘theme_bw’
plot_numeric_res_pred: no visible global function definition for
‘theme’
plot_numeric_res_pred: no visible global function definition for
‘ggplotly’
plot_twoclass_conf_mat: no visible global function definition for
‘augment’
plot_twoclass_conf_mat: no visible global function definition for
‘conf_mat’
plot_twoclass_conf_mat: no visible binding for global variable ‘Class’
plot_twoclass_conf_mat: no visible binding for global variable
‘.pred_class’
plot_twoclass_conf_mat: no visible global function definition for
‘autoplot’
plot_twoclass_obs_pred: no visible global function definition for
‘augment’
plot_twoclass_obs_pred: no visible global function definition for
‘ggplot’
plot_twoclass_obs_pred: no visible global function definition for ‘aes’
plot_twoclass_obs_pred: no visible global function definition for
‘geom_histogram’
plot_twoclass_obs_pred: no visible global function definition for
‘facet_wrap’
plot_twoclass_obs_pred: no visible global function definition for
‘labeller’
plot_twoclass_obs_pred: no visible binding for global variable
‘label_both’
plot_twoclass_obs_pred: no visible global function definition for
‘labs’
plot_twoclass_obs_pred: no visible global function definition for
‘lims’
plot_twoclass_pr: no visible global function definition for ‘augment’
plot_twoclass_pr: no visible global function definition for ‘pr_curve’
plot_twoclass_pr: no visible binding for global variable ‘Class’
plot_twoclass_pr: no visible global function definition for ‘mutate’
plot_twoclass_pr: no visible binding for global variable ‘.threshold’
plot_twoclass_pr: no visible global function definition for ‘arrange’
plot_twoclass_pr: no visible binding for global variable ‘delta’
plot_twoclass_pr: no visible global function definition for ‘slice’
plot_twoclass_pr: no visible global function definition for ‘autoplot’
plot_twoclass_pr: no visible global function definition for
‘geom_point’
plot_twoclass_pr: no visible global function definition for ‘aes’
plot_twoclass_pr: no visible binding for global variable ‘specificity’
plot_twoclass_pr: no visible binding for global variable ‘sensitivity’
plot_twoclass_pred_factorcol: no visible global function definition for
‘mutate’
plot_twoclass_pred_factorcol: no visible global function definition for
‘:=’
plot_twoclass_pred_factorcol: no visible global function definition for
‘case_when’
plot_twoclass_pred_factorcol: no visible global function definition for
‘ggplot’
plot_twoclass_pred_factorcol: no visible global function definition for
‘aes’
plot_twoclass_pred_factorcol: no visible global function definition for
‘sym’
plot_twoclass_pred_factorcol: no visible global function definition for
‘geom_point’
plot_twoclass_pred_factorcol: no visible binding for global variable
‘.color’
plot_twoclass_pred_factorcol: no visible global function definition for
‘facet_wrap’
plot_twoclass_pred_factorcol: no visible global function definition for
‘labeller’
plot_twoclass_pred_factorcol: no visible binding for global variable
‘label_both’
plot_twoclass_pred_factorcol: no visible global function definition for
‘scale_color_identity’
plot_twoclass_pred_factorcol: no visible global function definition for
‘labs’
plot_twoclass_pred_factorcol: no visible global function definition for
‘theme_bw’
plot_twoclass_pred_factorcol: no visible global function definition for
‘theme’
plot_twoclass_pred_factorcol: no visible global function definition for
‘ggplotly’
plot_twoclass_pred_numcol: no visible global function definition for
‘mutate’
plot_twoclass_pred_numcol: no visible global function definition for
‘:=’
plot_twoclass_pred_numcol: no visible global function definition for
‘case_when’
plot_twoclass_pred_numcol: no visible global function definition for
‘ggplot’
plot_twoclass_pred_numcol: no visible global function definition for
‘aes’
plot_twoclass_pred_numcol: no visible global function definition for
‘sym’
plot_twoclass_pred_numcol: no visible global function definition for
‘geom_point’
plot_twoclass_pred_numcol: no visible binding for global variable
‘.color’
plot_twoclass_pred_numcol: no visible global function definition for
‘facet_wrap’
plot_twoclass_pred_numcol: no visible global function definition for
‘labeller’
plot_twoclass_pred_numcol: no visible binding for global variable
‘label_both’
plot_twoclass_pred_numcol: no visible global function definition for
‘scale_color_identity’
plot_twoclass_pred_numcol: no visible global function definition for
‘labs’
plot_twoclass_pred_numcol: no visible global function definition for
‘theme_bw’
plot_twoclass_pred_numcol: no visible global function definition for
‘theme’
plot_twoclass_pred_numcol: no visible global function definition for
‘ggplotly’
plot_twoclass_roc: no visible global function definition for ‘augment’
plot_twoclass_roc: no visible global function definition for
‘roc_curve’
plot_twoclass_roc: no visible binding for global variable ‘Class’
plot_twoclass_roc: no visible global function definition for ‘mutate’
plot_twoclass_roc: no visible binding for global variable ‘.threshold’
plot_twoclass_roc: no visible global function definition for ‘arrange’
plot_twoclass_roc: no visible binding for global variable ‘delta’
plot_twoclass_roc: no visible global function definition for ‘slice’
plot_twoclass_roc: no visible global function definition for ‘autoplot’
plot_twoclass_roc: no visible global function definition for
‘geom_point’
plot_twoclass_roc: no visible global function definition for ‘aes’
plot_twoclass_roc: no visible binding for global variable ‘specificity’
plot_twoclass_roc: no visible binding for global variable ‘sensitivity’
Undefined global functions or variables:
.color .get_tune_outcome_names .pred .pred_class .residual .threshold
:= Class add_rowindex aes arrange augment autoplot case_when
collect_predictions conf_mat coord_obs_pred delta facet_wrap
geom_abline geom_histogram geom_point ggplot ggplotly inner_join
label_both labeller labs lims mutate pr_curve reorder roc_curve
scale_color_identity select sensitivity slice specificity sym theme
theme_bw
Consider adding
importFrom("stats", "reorder")
to your NAMESPACE file.
── Test failures ───────────────────────────────────────────────── testthat ────
> library(testthat)
Warning message:
Can't find generic `testthat_print` in package testthat to register S3 method.
i This message is only shown to developers using devtools.
i Do you need to update testthat to the latest version?
> library(shinymodels)
>
> test_check("shinymodels")
── Attaching packages ────────────────────────────────────── tidymodels 0.1.3 ──
✓ broom 0.7.8 ✓ recipes 0.1.16
✓ dials 0.0.9.9000 ✓ rsample 0.1.0
✓ dplyr 1.0.7 ✓ tibble 3.1.2
✓ ggplot2 3.3.4 ✓ tidyr 1.1.3
✓ infer 0.5.4 ✓ tune 0.1.5.9001
✓ modeldata 0.1.0 ✓ workflows 0.2.2.9000
✓ parsnip 0.1.6.9000 ✓ workflowsets 0.0.2.9000
✓ purrr 0.3.4 ✓ yardstick 0.0.8
── Conflicts ───────────────────────────────────────── tidymodels_conflicts() ──
x purrr::discard() masks scales::discard()
x dplyr::filter() masks stats::filter()
x purrr::is_null() masks testthat::is_null()
x dplyr::lag() masks stats::lag()
x tidyr::matches() masks rsample::matches(), dplyr::matches(), testthat::matches()
x recipes::step() masks stats::step()
• Use tidymodels_prefer() to resolve common conflicts.
══ Warnings ════════════════════════════════════════════════════════════════════
── Warning (test-first_level.R:5:1): (code run outside of `test_that()`) ───────
data set 'ad_data' not found
Backtrace:
1. utils::data(ad_data) test-first_level.R:5:0
── Warning (test-first_level_prob_name.R:5:1): (code run outside of `test_that()`) ──
data set 'ad_data' not found
Backtrace:
1. utils::data(ad_data) test-first_level_prob_name.R:5:0
══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test-first_level.R:7:1): (code run outside of `test_that()`) ─────────
Error: could not find function ".get_tune_outcome_names"
Backtrace:
▆
1. └─shinymodels::organize_data(ad_data_boost_res, ad_data) test-first_level.R:7:0
── Error (test-first_level_prob_name.R:7:1): (code run outside of `test_that()`) ──
Error: could not find function ".get_tune_outcome_names"
Backtrace:
▆
1. └─shinymodels::organize_data(ad_data_boost_res, ad_data) test-first_level_prob_name.R:7:0
── Error (test-organize_data.R:32:3): can accurately organize data ─────────────
Error: No `collect_predictions()` exists for this type of object.
Backtrace:
▆
1. ├─testthat::expect_error(organize_data(lin_mod, mtcars), "res_object should be a fit_resamples() object") test-organize_data.R:32:2
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat:::.capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─shinymodels::organize_data(lin_mod, mtcars)
8. ├─tune::collect_predictions(res_object, summarize = TRUE)
9. └─tune:::collect_predictions.default(res_object, summarize = TRUE) /Users/max/github/tune/R/collect.R:87:2
[ FAIL 3 | WARN 2 | SKIP 0 | PASS 3 ]
Error: Test failures
Execution halted
1 error x | 5 warnings x | 3 notes x
Error: R CMD check found ERRORs
Execution halted
Exited with status 1.
Co-authored-by: Max Kuhn <mxkuhn@gmail.com>
Co-authored-by: Max Kuhn <mxkuhn@gmail.com>
Co-authored-by: Max Kuhn <mxkuhn@gmail.com>
Co-authored-by: Max Kuhn <mxkuhn@gmail.com>
Co-authored-by: Max Kuhn <mxkuhn@gmail.com>
Merge branch 'initial_plot_functions' of https://github.com/adhikars11/shinymodels into initial_plot_functions # Conflicts: # tests/testthat/test-first_level.R
This pull request has been automatically locked. If you believe you have found a related problem, please file a new issue (with a reprex: https://reprex.tidyverse.org) and link to this issue. |
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